fixes JAL-778 - flag to indicate binding between an alignment panel and Jmol view...

[jalview.git] / src / jalview / schemabinding / version2 / Viewport.java

diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java
index aa97a95..49b0db2 100755 (executable)
--- a/src/jalview/schemabinding/version2/Viewport.java
+++ b/src/jalview/schemabinding/version2/Viewport.java
@@ -117,6 +117,16 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_showColourText;\r
 \r
     /**\r
+     * Field _showUnconserved.\r
+     */\r
+    private boolean _showUnconserved = false;\r
+\r
+    /**\r
+     * keeps track of state for field: _showUnconserved\r
+     */\r
+    private boolean _has_showUnconserved;\r
+\r
+    /**\r
      * Field _showBoxes.\r
      */\r
     private boolean _showBoxes;\r
@@ -157,6 +167,46 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_showSequenceFeatures;\r
 \r
     /**\r
+     * Field _showNPfeatureTooltip.\r
+     */\r
+    private boolean _showNPfeatureTooltip;\r
+\r
+    /**\r
+     * keeps track of state for field: _showNPfeatureTooltip\r
+     */\r
+    private boolean _has_showNPfeatureTooltip;\r
+\r
+    /**\r
+     * Field _showDbRefTooltip.\r
+     */\r
+    private boolean _showDbRefTooltip;\r
+\r
+    /**\r
+     * keeps track of state for field: _showDbRefTooltip\r
+     */\r
+    private boolean _has_showDbRefTooltip;\r
+\r
+    /**\r
+     * Field _followHighlight.\r
+     */\r
+    private boolean _followHighlight = true;\r
+\r
+    /**\r
+     * keeps track of state for field: _followHighlight\r
+     */\r
+    private boolean _has_followHighlight;\r
+\r
+    /**\r
+     * Field _followSelection.\r
+     */\r
+    private boolean _followSelection = true;\r
+\r
+    /**\r
+     * keeps track of state for field: _followSelection\r
+     */\r
+    private boolean _has_followSelection;\r
+\r
+    /**\r
      * Field _showAnnotation.\r
      */\r
     private boolean _showAnnotation;\r
@@ -167,6 +217,66 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_showAnnotation;\r
 \r
     /**\r
+     * Field _centreColumnLabels.\r
+     */\r
+    private boolean _centreColumnLabels = false;\r
+\r
+    /**\r
+     * keeps track of state for field: _centreColumnLabels\r
+     */\r
+    private boolean _has_centreColumnLabels;\r
+\r
+    /**\r
+     * Field _showGroupConservation.\r
+     */\r
+    private boolean _showGroupConservation = false;\r
+\r
+    /**\r
+     * keeps track of state for field: _showGroupConservation\r
+     */\r
+    private boolean _has_showGroupConservation;\r
+\r
+    /**\r
+     * Field _showGroupConsensus.\r
+     */\r
+    private boolean _showGroupConsensus = false;\r
+\r
+    /**\r
+     * keeps track of state for field: _showGroupConsensus\r
+     */\r
+    private boolean _has_showGroupConsensus;\r
+\r
+    /**\r
+     * Field _showConsensusHistogram.\r
+     */\r
+    private boolean _showConsensusHistogram = true;\r
+\r
+    /**\r
+     * keeps track of state for field: _showConsensusHistogram\r
+     */\r
+    private boolean _has_showConsensusHistogram;\r
+\r
+    /**\r
+     * Field _showSequenceLogo.\r
+     */\r
+    private boolean _showSequenceLogo = false;\r
+\r
+    /**\r
+     * keeps track of state for field: _showSequenceLogo\r
+     */\r
+    private boolean _has_showSequenceLogo;\r
+\r
+    /**\r
+     * Field _ignoreGapsinConsensus.\r
+     */\r
+    private boolean _ignoreGapsinConsensus = true;\r
+\r
+    /**\r
+     * keeps track of state for field: _ignoreGapsinConsensus\r
+     */\r
+    private boolean _has_ignoreGapsinConsensus;\r
+\r
+    /**\r
      * Field _xpos.\r
      */\r
     private int _xpos;\r
@@ -302,6 +412,13 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_textColThreshold;\r
 \r
     /**\r
+     * unique id used by jalview to synchronize between stored and\r
+     * instantiated views\r
+     *  \r
+     */\r
+    private java.lang.String _id;\r
+\r
+    /**\r
      * Field _annotationColours.\r
      */\r
     private jalview.schemabinding.version2.AnnotationColours _annotationColours;\r
@@ -356,6 +473,13 @@ public class Viewport implements java.io.Serializable {
 \r
     /**\r
      */\r
+    public void deleteCentreColumnLabels(\r
+    ) {\r
+        this._has_centreColumnLabels= false;\r
+    }\r
+\r
+    /**\r
+     */\r
     public void deleteConsThreshold(\r
     ) {\r
         this._has_consThreshold= false;\r
@@ -370,6 +494,20 @@ public class Viewport implements java.io.Serializable {
 \r
     /**\r
      */\r
+    public void deleteFollowHighlight(\r
+    ) {\r
+        this._has_followHighlight= false;\r
+    }\r
+\r
+    /**\r
+     */\r
+    public void deleteFollowSelection(\r
+    ) {\r
+        this._has_followSelection= false;\r
+    }\r
+\r
+    /**\r
+     */\r
     public void deleteFontSize(\r
     ) {\r
         this._has_fontSize= false;\r
@@ -398,6 +536,13 @@ public class Viewport implements java.io.Serializable {
 \r
     /**\r
      */\r
+    public void deleteIgnoreGapsinConsensus(\r
+    ) {\r
+        this._has_ignoreGapsinConsensus= false;\r
+    }\r
+\r
+    /**\r
+     */\r
     public void deletePidSelected(\r
     ) {\r
         this._has_pidSelected= false;\r
@@ -447,6 +592,20 @@ public class Viewport implements java.io.Serializable {
 \r
     /**\r
      */\r
+    public void deleteShowConsensusHistogram(\r
+    ) {\r
+        this._has_showConsensusHistogram= false;\r
+    }\r
+\r
+    /**\r
+     */\r
+    public void deleteShowDbRefTooltip(\r
+    ) {\r
+        this._has_showDbRefTooltip= false;\r
+    }\r
+\r
+    /**\r
+     */\r
     public void deleteShowFullId(\r
     ) {\r
         this._has_showFullId= false;\r
@@ -454,6 +613,27 @@ public class Viewport implements java.io.Serializable {
 \r
     /**\r
      */\r
+    public void deleteShowGroupConsensus(\r
+    ) {\r
+        this._has_showGroupConsensus= false;\r
+    }\r
+\r
+    /**\r
+     */\r
+    public void deleteShowGroupConservation(\r
+    ) {\r
+        this._has_showGroupConservation= false;\r
+    }\r
+\r
+    /**\r
+     */\r
+    public void deleteShowNPfeatureTooltip(\r
+    ) {\r
+        this._has_showNPfeatureTooltip= false;\r
+    }\r
+\r
+    /**\r
+     */\r
     public void deleteShowSequenceFeatures(\r
     ) {\r
         this._has_showSequenceFeatures= false;\r
@@ -461,6 +641,13 @@ public class Viewport implements java.io.Serializable {
 \r
     /**\r
      */\r
+    public void deleteShowSequenceLogo(\r
+    ) {\r
+        this._has_showSequenceLogo= false;\r
+    }\r
+\r
+    /**\r
+     */\r
     public void deleteShowText(\r
     ) {\r
         this._has_showText= false;\r
@@ -468,6 +655,13 @@ public class Viewport implements java.io.Serializable {
 \r
     /**\r
      */\r
+    public void deleteShowUnconserved(\r
+    ) {\r
+        this._has_showUnconserved= false;\r
+    }\r
+\r
+    /**\r
+     */\r
     public void deleteStartRes(\r
     ) {\r
         this._has_startRes= false;\r
@@ -561,6 +755,16 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Returns the value of field 'centreColumnLabels'.\r
+     * \r
+     * @return the value of field 'CentreColumnLabels'.\r
+     */\r
+    public boolean getCentreColumnLabels(\r
+    ) {\r
+        return this._centreColumnLabels;\r
+    }\r
+\r
+    /**\r
      * Returns the value of field 'consThreshold'.\r
      * \r
      * @return the value of field 'ConsThreshold'.\r
@@ -581,6 +785,26 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Returns the value of field 'followHighlight'.\r
+     * \r
+     * @return the value of field 'FollowHighlight'.\r
+     */\r
+    public boolean getFollowHighlight(\r
+    ) {\r
+        return this._followHighlight;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'followSelection'.\r
+     * \r
+     * @return the value of field 'FollowSelection'.\r
+     */\r
+    public boolean getFollowSelection(\r
+    ) {\r
+        return this._followSelection;\r
+    }\r
+\r
+    /**\r
      * Returns the value of field 'fontName'.\r
      * \r
      * @return the value of field 'FontName'.\r
@@ -678,6 +902,29 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Returns the value of field 'id'. The field 'id' has the\r
+     * following description: unique id used by jalview to\r
+     * synchronize between stored and instantiated views\r
+     *  \r
+     * \r
+     * @return the value of field 'Id'.\r
+     */\r
+    public java.lang.String getId(\r
+    ) {\r
+        return this._id;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'ignoreGapsinConsensus'.\r
+     * \r
+     * @return the value of field 'IgnoreGapsinConsensus'.\r
+     */\r
+    public boolean getIgnoreGapsinConsensus(\r
+    ) {\r
+        return this._ignoreGapsinConsensus;\r
+    }\r
+\r
+    /**\r
      * Returns the value of field 'pidSelected'.\r
      * \r
      * @return the value of field 'PidSelected'.\r
@@ -758,6 +1005,26 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Returns the value of field 'showConsensusHistogram'.\r
+     * \r
+     * @return the value of field 'ShowConsensusHistogram'.\r
+     */\r
+    public boolean getShowConsensusHistogram(\r
+    ) {\r
+        return this._showConsensusHistogram;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'showDbRefTooltip'.\r
+     * \r
+     * @return the value of field 'ShowDbRefTooltip'.\r
+     */\r
+    public boolean getShowDbRefTooltip(\r
+    ) {\r
+        return this._showDbRefTooltip;\r
+    }\r
+\r
+    /**\r
      * Returns the value of field 'showFullId'.\r
      * \r
      * @return the value of field 'ShowFullId'.\r
@@ -768,6 +1035,36 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Returns the value of field 'showGroupConsensus'.\r
+     * \r
+     * @return the value of field 'ShowGroupConsensus'.\r
+     */\r
+    public boolean getShowGroupConsensus(\r
+    ) {\r
+        return this._showGroupConsensus;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'showGroupConservation'.\r
+     * \r
+     * @return the value of field 'ShowGroupConservation'.\r
+     */\r
+    public boolean getShowGroupConservation(\r
+    ) {\r
+        return this._showGroupConservation;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'showNPfeatureTooltip'.\r
+     * \r
+     * @return the value of field 'ShowNPfeatureTooltip'.\r
+     */\r
+    public boolean getShowNPfeatureTooltip(\r
+    ) {\r
+        return this._showNPfeatureTooltip;\r
+    }\r
+\r
+    /**\r
      * Returns the value of field 'showSequenceFeatures'.\r
      * \r
      * @return the value of field 'ShowSequenceFeatures'.\r
@@ -778,6 +1075,16 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Returns the value of field 'showSequenceLogo'.\r
+     * \r
+     * @return the value of field 'ShowSequenceLogo'.\r
+     */\r
+    public boolean getShowSequenceLogo(\r
+    ) {\r
+        return this._showSequenceLogo;\r
+    }\r
+\r
+    /**\r
      * Returns the value of field 'showText'.\r
      * \r
      * @return the value of field 'ShowText'.\r
@@ -788,6 +1095,16 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Returns the value of field 'showUnconserved'.\r
+     * \r
+     * @return the value of field 'ShowUnconserved'.\r
+     */\r
+    public boolean getShowUnconserved(\r
+    ) {\r
+        return this._showUnconserved;\r
+    }\r
+\r
+    /**\r
      * Returns the value of field 'startRes'.\r
      * \r
      * @return the value of field 'StartRes'.\r
@@ -898,6 +1215,16 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Method hasCentreColumnLabels.\r
+     * \r
+     * @return true if at least one CentreColumnLabels has been adde\r
+     */\r
+    public boolean hasCentreColumnLabels(\r
+    ) {\r
+        return this._has_centreColumnLabels;\r
+    }\r
+\r
+    /**\r
      * Method hasConsThreshold.\r
      * \r
      * @return true if at least one ConsThreshold has been added\r
@@ -919,6 +1246,26 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Method hasFollowHighlight.\r
+     * \r
+     * @return true if at least one FollowHighlight has been added\r
+     */\r
+    public boolean hasFollowHighlight(\r
+    ) {\r
+        return this._has_followHighlight;\r
+    }\r
+\r
+    /**\r
+     * Method hasFollowSelection.\r
+     * \r
+     * @return true if at least one FollowSelection has been added\r
+     */\r
+    public boolean hasFollowSelection(\r
+    ) {\r
+        return this._has_followSelection;\r
+    }\r
+\r
+    /**\r
      * Method hasFontSize.\r
      * \r
      * @return true if at least one FontSize has been added\r
@@ -959,6 +1306,17 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Method hasIgnoreGapsinConsensus.\r
+     * \r
+     * @return true if at least one IgnoreGapsinConsensus has been\r
+     * added\r
+     */\r
+    public boolean hasIgnoreGapsinConsensus(\r
+    ) {\r
+        return this._has_ignoreGapsinConsensus;\r
+    }\r
+\r
+    /**\r
      * Method hasPidSelected.\r
      * \r
      * @return true if at least one PidSelected has been added\r
@@ -1029,6 +1387,27 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Method hasShowConsensusHistogram.\r
+     * \r
+     * @return true if at least one ShowConsensusHistogram has been\r
+     * added\r
+     */\r
+    public boolean hasShowConsensusHistogram(\r
+    ) {\r
+        return this._has_showConsensusHistogram;\r
+    }\r
+\r
+    /**\r
+     * Method hasShowDbRefTooltip.\r
+     * \r
+     * @return true if at least one ShowDbRefTooltip has been added\r
+     */\r
+    public boolean hasShowDbRefTooltip(\r
+    ) {\r
+        return this._has_showDbRefTooltip;\r
+    }\r
+\r
+    /**\r
      * Method hasShowFullId.\r
      * \r
      * @return true if at least one ShowFullId has been added\r
@@ -1039,6 +1418,38 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Method hasShowGroupConsensus.\r
+     * \r
+     * @return true if at least one ShowGroupConsensus has been adde\r
+     */\r
+    public boolean hasShowGroupConsensus(\r
+    ) {\r
+        return this._has_showGroupConsensus;\r
+    }\r
+\r
+    /**\r
+     * Method hasShowGroupConservation.\r
+     * \r
+     * @return true if at least one ShowGroupConservation has been\r
+     * added\r
+     */\r
+    public boolean hasShowGroupConservation(\r
+    ) {\r
+        return this._has_showGroupConservation;\r
+    }\r
+\r
+    /**\r
+     * Method hasShowNPfeatureTooltip.\r
+     * \r
+     * @return true if at least one ShowNPfeatureTooltip has been\r
+     * added\r
+     */\r
+    public boolean hasShowNPfeatureTooltip(\r
+    ) {\r
+        return this._has_showNPfeatureTooltip;\r
+    }\r
+\r
+    /**\r
      * Method hasShowSequenceFeatures.\r
      * \r
      * @return true if at least one ShowSequenceFeatures has been\r
@@ -1050,6 +1461,16 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Method hasShowSequenceLogo.\r
+     * \r
+     * @return true if at least one ShowSequenceLogo has been added\r
+     */\r
+    public boolean hasShowSequenceLogo(\r
+    ) {\r
+        return this._has_showSequenceLogo;\r
+    }\r
+\r
+    /**\r
      * Method hasShowText.\r
      * \r
      * @return true if at least one ShowText has been added\r
@@ -1060,6 +1481,16 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Method hasShowUnconserved.\r
+     * \r
+     * @return true if at least one ShowUnconserved has been added\r
+     */\r
+    public boolean hasShowUnconserved(\r
+    ) {\r
+        return this._has_showUnconserved;\r
+    }\r
+\r
+    /**\r
      * Method hasStartRes.\r
      * \r
      * @return true if at least one StartRes has been added\r
@@ -1150,6 +1581,16 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Returns the value of field 'centreColumnLabels'.\r
+     * \r
+     * @return the value of field 'CentreColumnLabels'.\r
+     */\r
+    public boolean isCentreColumnLabels(\r
+    ) {\r
+        return this._centreColumnLabels;\r
+    }\r
+\r
+    /**\r
      * Returns the value of field 'conservationSelected'.\r
      * \r
      * @return the value of field 'ConservationSelected'.\r
@@ -1160,6 +1601,26 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Returns the value of field 'followHighlight'.\r
+     * \r
+     * @return the value of field 'FollowHighlight'.\r
+     */\r
+    public boolean isFollowHighlight(\r
+    ) {\r
+        return this._followHighlight;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'followSelection'.\r
+     * \r
+     * @return the value of field 'FollowSelection'.\r
+     */\r
+    public boolean isFollowSelection(\r
+    ) {\r
+        return this._followSelection;\r
+    }\r
+\r
+    /**\r
      * Returns the value of field 'gatheredViews'.\r
      * \r
      * @return the value of field 'GatheredViews'.\r
@@ -1170,6 +1631,16 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Returns the value of field 'ignoreGapsinConsensus'.\r
+     * \r
+     * @return the value of field 'IgnoreGapsinConsensus'.\r
+     */\r
+    public boolean isIgnoreGapsinConsensus(\r
+    ) {\r
+        return this._ignoreGapsinConsensus;\r
+    }\r
+\r
+    /**\r
      * Returns the value of field 'pidSelected'.\r
      * \r
      * @return the value of field 'PidSelected'.\r
@@ -1230,6 +1701,26 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Returns the value of field 'showConsensusHistogram'.\r
+     * \r
+     * @return the value of field 'ShowConsensusHistogram'.\r
+     */\r
+    public boolean isShowConsensusHistogram(\r
+    ) {\r
+        return this._showConsensusHistogram;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'showDbRefTooltip'.\r
+     * \r
+     * @return the value of field 'ShowDbRefTooltip'.\r
+     */\r
+    public boolean isShowDbRefTooltip(\r
+    ) {\r
+        return this._showDbRefTooltip;\r
+    }\r
+\r
+    /**\r
      * Returns the value of field 'showFullId'.\r
      * \r
      * @return the value of field 'ShowFullId'.\r
@@ -1240,6 +1731,36 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Returns the value of field 'showGroupConsensus'.\r
+     * \r
+     * @return the value of field 'ShowGroupConsensus'.\r
+     */\r
+    public boolean isShowGroupConsensus(\r
+    ) {\r
+        return this._showGroupConsensus;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'showGroupConservation'.\r
+     * \r
+     * @return the value of field 'ShowGroupConservation'.\r
+     */\r
+    public boolean isShowGroupConservation(\r
+    ) {\r
+        return this._showGroupConservation;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'showNPfeatureTooltip'.\r
+     * \r
+     * @return the value of field 'ShowNPfeatureTooltip'.\r
+     */\r
+    public boolean isShowNPfeatureTooltip(\r
+    ) {\r
+        return this._showNPfeatureTooltip;\r
+    }\r
+\r
+    /**\r
      * Returns the value of field 'showSequenceFeatures'.\r
      * \r
      * @return the value of field 'ShowSequenceFeatures'.\r
@@ -1250,6 +1771,16 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Returns the value of field 'showSequenceLogo'.\r
+     * \r
+     * @return the value of field 'ShowSequenceLogo'.\r
+     */\r
+    public boolean isShowSequenceLogo(\r
+    ) {\r
+        return this._showSequenceLogo;\r
+    }\r
+\r
+    /**\r
      * Returns the value of field 'showText'.\r
      * \r
      * @return the value of field 'ShowText'.\r
@@ -1260,6 +1791,16 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Returns the value of field 'showUnconserved'.\r
+     * \r
+     * @return the value of field 'ShowUnconserved'.\r
+     */\r
+    public boolean isShowUnconserved(\r
+    ) {\r
+        return this._showUnconserved;\r
+    }\r
+\r
+    /**\r
      * Method isValid.\r
      * \r
      * @return true if this object is valid according to the schema\r
@@ -1369,6 +1910,18 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Sets the value of field 'centreColumnLabels'.\r
+     * \r
+     * @param centreColumnLabels the value of field\r
+     * 'centreColumnLabels'.\r
+     */\r
+    public void setCentreColumnLabels(\r
+            final boolean centreColumnLabels) {\r
+        this._centreColumnLabels = centreColumnLabels;\r
+        this._has_centreColumnLabels = true;\r
+    }\r
+\r
+    /**\r
      * Sets the value of field 'consThreshold'.\r
      * \r
      * @param consThreshold the value of field 'consThreshold'.\r
@@ -1392,6 +1945,28 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Sets the value of field 'followHighlight'.\r
+     * \r
+     * @param followHighlight the value of field 'followHighlight'.\r
+     */\r
+    public void setFollowHighlight(\r
+            final boolean followHighlight) {\r
+        this._followHighlight = followHighlight;\r
+        this._has_followHighlight = true;\r
+    }\r
+\r
+    /**\r
+     * Sets the value of field 'followSelection'.\r
+     * \r
+     * @param followSelection the value of field 'followSelection'.\r
+     */\r
+    public void setFollowSelection(\r
+            final boolean followSelection) {\r
+        this._followSelection = followSelection;\r
+        this._has_followSelection = true;\r
+    }\r
+\r
+    /**\r
      * Sets the value of field 'fontName'.\r
      * \r
      * @param fontName the value of field 'fontName'.\r
@@ -1481,6 +2056,31 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Sets the value of field 'id'. The field 'id' has the\r
+     * following description: unique id used by jalview to\r
+     * synchronize between stored and instantiated views\r
+     *  \r
+     * \r
+     * @param id the value of field 'id'.\r
+     */\r
+    public void setId(\r
+            final java.lang.String id) {\r
+        this._id = id;\r
+    }\r
+\r
+    /**\r
+     * Sets the value of field 'ignoreGapsinConsensus'.\r
+     * \r
+     * @param ignoreGapsinConsensus the value of field\r
+     * 'ignoreGapsinConsensus'.\r
+     */\r
+    public void setIgnoreGapsinConsensus(\r
+            final boolean ignoreGapsinConsensus) {\r
+        this._ignoreGapsinConsensus = ignoreGapsinConsensus;\r
+        this._has_ignoreGapsinConsensus = true;\r
+    }\r
+\r
+    /**\r
      * Sets the value of field 'pidSelected'.\r
      * \r
      * @param pidSelected the value of field 'pidSelected'.\r
@@ -1568,6 +2168,29 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Sets the value of field 'showConsensusHistogram'.\r
+     * \r
+     * @param showConsensusHistogram the value of field\r
+     * 'showConsensusHistogram'.\r
+     */\r
+    public void setShowConsensusHistogram(\r
+            final boolean showConsensusHistogram) {\r
+        this._showConsensusHistogram = showConsensusHistogram;\r
+        this._has_showConsensusHistogram = true;\r
+    }\r
+\r
+    /**\r
+     * Sets the value of field 'showDbRefTooltip'.\r
+     * \r
+     * @param showDbRefTooltip the value of field 'showDbRefTooltip'\r
+     */\r
+    public void setShowDbRefTooltip(\r
+            final boolean showDbRefTooltip) {\r
+        this._showDbRefTooltip = showDbRefTooltip;\r
+        this._has_showDbRefTooltip = true;\r
+    }\r
+\r
+    /**\r
      * Sets the value of field 'showFullId'.\r
      * \r
      * @param showFullId the value of field 'showFullId'.\r
@@ -1579,6 +2202,42 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Sets the value of field 'showGroupConsensus'.\r
+     * \r
+     * @param showGroupConsensus the value of field\r
+     * 'showGroupConsensus'.\r
+     */\r
+    public void setShowGroupConsensus(\r
+            final boolean showGroupConsensus) {\r
+        this._showGroupConsensus = showGroupConsensus;\r
+        this._has_showGroupConsensus = true;\r
+    }\r
+\r
+    /**\r
+     * Sets the value of field 'showGroupConservation'.\r
+     * \r
+     * @param showGroupConservation the value of field\r
+     * 'showGroupConservation'.\r
+     */\r
+    public void setShowGroupConservation(\r
+            final boolean showGroupConservation) {\r
+        this._showGroupConservation = showGroupConservation;\r
+        this._has_showGroupConservation = true;\r
+    }\r
+\r
+    /**\r
+     * Sets the value of field 'showNPfeatureTooltip'.\r
+     * \r
+     * @param showNPfeatureTooltip the value of field\r
+     * 'showNPfeatureTooltip'.\r
+     */\r
+    public void setShowNPfeatureTooltip(\r
+            final boolean showNPfeatureTooltip) {\r
+        this._showNPfeatureTooltip = showNPfeatureTooltip;\r
+        this._has_showNPfeatureTooltip = true;\r
+    }\r
+\r
+    /**\r
      * Sets the value of field 'showSequenceFeatures'.\r
      * \r
      * @param showSequenceFeatures the value of field\r
@@ -1591,6 +2250,17 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Sets the value of field 'showSequenceLogo'.\r
+     * \r
+     * @param showSequenceLogo the value of field 'showSequenceLogo'\r
+     */\r
+    public void setShowSequenceLogo(\r
+            final boolean showSequenceLogo) {\r
+        this._showSequenceLogo = showSequenceLogo;\r
+        this._has_showSequenceLogo = true;\r
+    }\r
+\r
+    /**\r
      * Sets the value of field 'showText'.\r
      * \r
      * @param showText the value of field 'showText'.\r
@@ -1602,6 +2272,17 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Sets the value of field 'showUnconserved'.\r
+     * \r
+     * @param showUnconserved the value of field 'showUnconserved'.\r
+     */\r
+    public void setShowUnconserved(\r
+            final boolean showUnconserved) {\r
+        this._showUnconserved = showUnconserved;\r
+        this._has_showUnconserved = true;\r
+    }\r
+\r
+    /**\r
      * Sets the value of field 'startRes'.\r
      * \r
      * @param startRes the value of field 'startRes'.\r